I also use Concur and never had this happen until a couple of weeks ago. In my case, though, I had booked an itinerary and had to call to change it; since it was within 24 hours of the original booking, the agent cancelled it and started a new booking from scratch. When she ticketed it, the new reservation was "upgrade eligible" instead of "upgrade requested" and I didn't notice until OLCI, when I tweeted and it was quickly changed back. Luckily, it was JFK-LAX where advance upgrades are never handed out anyway.